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Brotherhood is not retelling the 'same basic story' if you're referring to the first anime. Brotherhood isn't the 'second season', it's a remake. The first anime's story is completely different from the manga's from Hughes' death, I've been told. BONES completely made up everything from that point on, I think. Brotherhood is going to follow the manga, which will obviously lead to the its own ending. Which, as a matter of fact, is drawing close.

You should go read the manga. Its story is simply amazing.

It changes completely after Bradley and his men take over Greed's hideout when Ed and Al are visiting Izumi actually. There were some slight differences from before that moment, but it's after Greed's first fight with Ed that things really start to change in the first anime. And yes, do read the manga. The first anime of FMA was like the story of Naruto without Akatsuki, for example, or Bleach without Soul Society (and it was still awesome, which says a lot about the manga).

Brotherhood is leaving some manga material out (for pacing/budget reasons, really), but the first anime literally did its own thing for the most part.

Let's put it this way: Nothing past ~chapter 30 (and not nearly everything from before chapter 30, and certainly not enough to be considered an adaptation trying to be faithful to the manga) of the manga was used in the first anime. A good deal of anime-original filler was created for FMA1 that has nothing to do with the manga canon, characters die in the show who aren't even dead yet in the manga (and vice versa), several of the homunculus (and other characters) were completely different, the main story is completely different, and many of the main characters in the first anime don't even exist at all in the manga (IE: Archer and Dante), and the majority of the characters that show up in the manga either have their roles greatly reduced or are omitted completely from the first anime.

Chapter 99 is the most recent chapter that has been released. The manga should finish within a year or so, at somewhere between 103-106 chapters (we're chest deep in the final arc).

Let's put it this way: Nothing past ~chapter 30 (and not nearly everything from before chapter 30, and certainly not enough to be considered an adaptation trying to be faithful to the manga) of the manga was used in the first anime.

Chapter 39 was the last chapter published before Episode 51 of the first anime series. They covered about as much as possible of what had been written at the time. This is what happens when a weekly show tries to cover a monthly series. Only 14 new chapters were published while the series aired. The last chapter published before the start of the show was chapter 25, so it's not surprising that the show only covered about that much material.

Chapter 39 was the last chapter published before Episode 51 of the first anime series. They covered about as much as possible of what had been written at the time. This is what happens when a weekly show tries to cover a monthly series. Only 14 new chapters were published while the series aired. The last chapter published before the start of the show was chapter 25, so it's not surprising that the show only covered about that much material.

It's not surprising but they also decided to make the series with so little material available at the time. Thus they knew this would happen and planned in the very beginning to make the first FMA series go in a different direction than the manga.

Even in the early episodes (that are more similar to the manga) you can see plot lines/characters not in the manga that would play a part in later parts of the first series. For example the appearance of Lyra in the coal mine episode.

First anime obviously had no idea what to do with Roy and his crew. Riza's character, who's so in-depth in the manga, was almost non-existant in it. And Falman, Breda and Fuery barely had personalities.

Well to be honest Roy was one of the few characters I liked in the first series (and I don't agree that he was only used for comic relief.) In fact my two favorite moments were between him and Ed.

Spoiler for 1st series:

1) When Roy gets angry at Ed for not trusting him and telling him what is going on so he could look out for Ed & Al
2) The last moment between Ed & Roy in the car

But that being said I was disappointed with what they did with the character in the movie. It's like he did a complete 180 in terms of character development that it made little sense. And I agree that they didn't seem to know what to do with Riza and the rest of the Roy crew.

Let's not forget that it was Roy who defeated Wrath in the first series (and Wrath was named Pride back then if I recall)(I'm talking about Bradley), so he was much more than a supporting character from that respect. And the fact that he declared all female personell ought to wear tiny miniskirts made him the best character in the first series.

Indeed. Right now, they're still around the same point as chapter 50 in the manga, so there's still ways to go as the manga's in chapter 99 and going on 100 now. If they have it planned for episode 63 being the end of it, that's another 38 episodes, meaning 38 weeks, meaning nine months and a half, meaning 9 more chapters in the manga. I think the manga will be over by then.